If you looking to do a proteomics study and you want a cell fractionation technique, here is an article that may be of use to you for your study.

However, I have never heard of a direct method for separating Euchromatin and Heterochromatin.

If necessary, consult others in your department

Thanks Michael for the article. I recently read an article describing the separation of Euchromatin from Heterochromatin using MNase digestion. Thus I wanted to have more ideas before choosing which protocol to choose.

@Maina, if your are looking for protocols that utilizes MNase digestion, attached are 2 that may help you

http://atm.skkumed.ac.kr/protocol/Micrococcal%20Nuclease%20Analysis.pdf

http://www.abcam.com/ps/pdf/protocols/N-ChIP.pdf

Michael this is really great thanks.

Glad I could help